Geneland: a computer package for landscape genetics

Geneland is a computer package that allows to make use of georeferenced individual multilocus genotypes for the inference of the number of populations and of the spatial location of genetic discontinuities between those populations. Main assumptions of the method are: (i) the number of populations is unknown and all values are considered a priori equally likely, (ii) populations are spread over areas given by a union of some polygons of unknown location in the spatial domain, (iii) Hardy–Weinberg equilibrium is assumed within each population and (iv) allele frequencies in each population are unknown and treated as random variable either following the so‐called Dirichlet model or Falush model. Different algorithms implemented in Geneland to perform inferences are first briefly presented. Then major running steps and outputs (i.e. histogram of number of populations and map of posterior probabilities of population membership) are illustrated from the analysis of a simulated data set, which was also produced by Geneland.     

SPECSTAT: PC software for statistical data analysis in the field of population genetics

This set of applied programs, SPECSTAT, has been written in Turbo Pascal-5 and is adapted for an IBM compatible PC-XT/AT using MS-DOS. SPECSTAT is a small software package (approximately 300K) which has high efficacy when performing calculations. SPECSTAT provides some new computational opportunities not provided by the existing statistical packages for analyzing allozyme population genetic data. Furthermore, it is able to carry out some simple transformations of quantitative traits (QT) and the genotypic data matrix. These transformations are convenient for the investigation of QT and allele frequencies and for the analysis of the correlations between QT and allozyme genotypic codes. From the vectors of genotypic codes for each sample, the following parameters are computed: i) the allele frequencies with standard errors (SE), ii) chi-squared values of goodness-of-fit for the observed and expected Hardy-Weinberg genotype frequencies and iii) H_o, H_s and F_is values. The H_t, F_it, F_st, D_st′ and F_st′ statistics, chi-squared values in the heterogeneity test of the predominant alleles, and G-statistics of all-allelic heterogeneity among samples with Williams' correction (Sokal & Rolf, 1981) are also available. Calculations are performed to produce single-locus and combined matrices of Nei's genetic distances Dn and Dm (standard and minimal unbiased), and the matrix of combined Kalabushkin's similarity metrics, which maximize small differences. Other computational opportunities are provided as well. Output data are simple ASCII files and are organized in a compact mode which can either be used directly for publication or used after minor changes in further calculations.     

ZFIQ: a software package for zebrafish biology

Rapid development, transparency and small size are the outstanding features of zebrafish that make it as an increasingly important vertebrate system for developmental biology, functional genomics, disease modeling and drug discovery. Zebrafish has been regarded as ideal animal specie for studying the relationship between genotype and phenotype, for pathway analysis and systems biology. However, the tremendous amount of data generated from large numbers of embryos has led to the bottleneck of data analysis and modeling. The zebrafish image quantitator (ZFIQ) software provides streamlined data processing and analysis capability for developmental biology and disease modeling using zebrafish model. AVAILABILITY: ZFIQ is available for download at http://www.cbi-platform.net.     

EXPERFARM: a new package in BASIC for teaching genetics

We have developed two interactive computer programs (togetherreferred to as EXPERFARM), which enable simulation of a greatvariety of genetic situations. This package is designed forteaching basic genetics as well as quantitative and populationgenetics. The main advantages of EXPERFARM are its great versatility,as different situations can be simulated by simply changingthe inputs, and the small amount of training necessary for theusers. Received on August 15, 1985; accepted on February 3, 1986     

SubpathwayMiner: a software package for flexible identification of pathways

With the development of high-throughput experimental techniques such as microarray, mass spectrometry and large-scale mutagenesis, there is an increasing need to automatically annotate gene sets and identify the involved pathways. Although many pathway analysis tools are developed, new tools are still needed to meet the requirements for flexible or advanced analysis purpose. Here, we developed an R-based software package (SubpathwayMiner) for flexible pathway identification. SubpathwayMiner facilitates sub-pathway identification of metabolic pathways by using pathway structure information. Additionally, SubpathwayMiner also provides more flexibility in annotating gene sets and identifying the involved pathways (entire pathways and sub-pathways): (i) SubpathwayMiner is able to provide the most up-to-date pathway analysis results for users; (ii) SubpathwayMiner supports multiple species (∼100 eukaryotes, 714 bacteria and 52 Archaea) and different gene identifiers (Entrez Gene IDs, NCBI-gi IDs, UniProt IDs, PDB IDs, etc.) in the KEGG GENE database; (iii) the system is quite efficient in cooperating with other R-based tools in biology. SubpathwayMiner is freely available at http://cran.r-project.org/web/packages/SubpathwayMiner/.     

BioBayes: a software package for Bayesian inference in systems biology

MOTIVATION: There are several levels of uncertainty involved in the mathematical modelling of biochemical systems. There often may be a degree of uncertainty about the values of kinetic parameters, about the general structure of the model and about the behaviour of biochemical species which cannot be observed directly. The methods of Bayesian inference provide a consistent framework for modelling and predicting in these uncertain conditions. We present a software package for applying the Bayesian inferential methodology to problems in systems biology. RESULTS: Described herein is a software package, BioBayes, which provides a framework for Bayesian parameter estimation and evidential model ranking over models of biochemical systems defined using ordinary differential equations. The package is extensible allowing additional modules to be included by developers. There are no other such packages available which provide this functionality.     

SNPbox: a modular software package for large-scale primer design

SUMMARY: We developed a modular software package SNPbox that automates and standardizes the generation of PCR primers and is used in the strategy for constructing single nucleotide polymorphisms (SNPs) maps. In this strategy, the focus of primer design can be either on the validation of annotated public SNPs or on the SNP discovery in exon regions or extended genomic regions, both by resequencing. SNPbox relies on Primer3 for the primer design and combines this program with other publicly available software tools such as BLAST, Spidey and RepeatMasker, and newly developed algorithms. Primer conditions were chosen such that PCR amplifications are uniform for each PCR amplicon facilitating the use of high-throughput genetic platforms. SNPbox can also be used for the design of primer sets for mutation analysis, STR marker genotyping and microarray oligo design. Of the 2500 primer sets designed by SNPbox, 95% successfully amplified genomic DNA under uniform PCR conditions. AVAILABILITY: The software is available from the authors upon request. SUPPLEMENTARY INFORMATION: SNPbox_supplement.     

Taxonome: a software package for linking biological species data

Online databases of biological information offer tremendous potential for evolutionary and ecological discoveries, especially if data are combined in novel ways. However, the different names and varied spellings used for many species present major barriers to linking data. Taxonome is a software tool designed to solve this problem by quickly and reproducibly matching biological names to a given reference set. It is available both as a graphical user interface (GUI) for simple interactive use, and as a library for more advanced functionality with programs written in Python. Taxonome also includes functions to standardize distribution information to a well‐defined set of regions, such as the TDWG World Geographical Scheme for Recording Plant Distributions. In combination, these tools will help biologists to rapidly synthesize disparate datasets, and to investigate large‐scale patterns in species traits.     

ISD: a software package for Bayesian NMR structure calculation

Summary: The conventional approach to calculating biomolecularstructures from nuclear magnetic resonance (NMR) data is oftenviewed as subjective due to its dependence on rules of thumbfor deriving geometric constraints and suitable values for theoryparameters from noisy experimental data. As a result, it canbe difficult to judge the precision of an NMR structure in anobjective manner. The inferential Structure determination (ISD)framework, which has been introduced recently, addresses thisproblem by using Bayesian inference to derive a probabilitydistribution that represents both the unknown structure andits uncertainty. It also determines additional unknowns, suchas theory parameters, that normally need to be chosen empirically.Here we give an overview of the ISD software package, whichimplements this methodology. Availability: http://www.bioc.cam.ac.uk/isd Contact: wolfgang.rieping{at}bioc.cam.ac.uk, michael.habeck{at}tuebingen.mpg.de Associate Editor: Alfonso Valencia     

introgress: a software package for mapping components of isolation in hybrids

A new software package (introgress) provides functions for analysing introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multi-locus genotype data and testing for deviations from neutral expectations. The software works with co-dominant, dominant and haploid marker data, and does not require fixed allelic differences between parental populations for the sampled genetic markers. Permutation and parametric procedures generate neutral expectations for introgression and provide a basis for significance tests of observed genomic clines. The software also implements maximum likelihood estimates of hybrid index from genotypic data and a number of graphical analyses. The package is an extension of the R statistical software, is written in the R language and is freely available through the Comprehensive R Archive Network (CRAN; http://cran.r-project.org/). In this study, we describe introgress and demonstrate its use with a sample data set.     

Mfuzz: a software package for soft clustering of microarray data

For the analysis of microarray data, clustering techniques are frequently used. Most of such methods are based on hard clustering of data wherein one gene (or sample) is assigned to exactly one cluster. Hard clustering, however, suffers from several drawbacks such as sensitivity to noise and information loss. In contrast, soft clustering methods can assign a gene to several clusters. They can overcome shortcomings of conventional hard clustering techniques and offer further advantages. Thus, we constructed an R package termed Mfuzz implementing soft clustering tools for microarray data analysis. The additional package Mfuzzgui provides a convenient TclTk based graphical user interface. AVAILABILITY: The R package Mfuzz and Mfuzzgui are available at http://itb1.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/index.html. Their distribution is subject to GPL version 2 license.     

HDX-analyzer: a novel package for statistical analysis of protein structure dynamics

BACKGROUND: HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure dynamics based on the mass increase of a protein of which the backbone protons exchanged with solvent deuterium. Coupled with enzyme digestion and MS/MS analysis, HDX mass spectrometry can be used to study the regional dynamics of protein based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments. Various software packages have been developed to analyze HDX mass spectrometry data. Despite the progresses, proper and explicit statistical treatment is still lacking in most of the current HDX mass spectrometry software. In order to address this issue, we have developed the HDXanalyzer for the statistical analysis of HDX mass spectrometry data using R, Python, and RPY2. IMPLEMENTATION AND RESULTS: HDXanalyzer package contains three major modules, the data processing module, the statistical analysis module, and the user interface. RPY2 is employed to enable the connection of these three components, where the data processing module is implemented using Python and the statistical analysis module is implemented with R. RPY2 creates a low-level interface for R and allows the effective integration of statistical module for data processing. The data processing module generates the centroid for the peptides in form of m/z value, and the differences of centroids between the peptides derived from apo and ligand-bound protein allow us to evaluate whether the regions have significant changes in structure dynamics or not. Another option of the software is to calculate the deuterium incorporation rate for the comparison. The two types of statistical analyses are Paired Student's t-test and the linear combination of the intercept for multiple regression and ANCOVA model. The user interface is implemented with wxpython to facilitate the data visualization in graphs and the statistical analysis output presentation. In order to evaluate the software, a previously published xylanase HDX mass spectrometry analysis dataset is processed and presented. The results from the different statistical analysis methods are compared and shown to be similar. The statistical analysis results are overlaid with the three dimensional structure of the protein to highlight the regional structure dynamics changes in the xylanase enzyme. CONCLUSION: Statistical analysis provides crucial evaluation of whether a protein region is significantly protected or unprotected during the HDX mass spectrometry studies. Although there are several other available software programs to process HDX experimental data, HDXanalyzer is the first software program to offer multiple statistical methods to evaluate the changes in protein structure dynamics based on HDX mass spectrometry analysis. Moreover, the statistical analysis can be carried out for both m/z value and deuterium incorporation rate. In addition, the software package can be used for the data generated from a wide range of mass spectrometry instruments.     

POLDISP: a software package for indirect estimation of contemporary pollen dispersal

poldisp 1.0 is a free software package to estimate the distribution of pollen dispersal distances from mother–offspring diploid genotypic data. It requires the spatial coordinates and genotypes of a sample of seed plants and their respective maternal progenies, providing estimates of the average, variance and kurtosis of the pollen dispersal curve. poldisp also estimates the effective reproductive density of pollen donors and the correlation of paternity within and among maternal sibships. poldisp is useful for characterizing the spatial scale of pollen dispersal, for assessing the variation in male fertility and for investigating biological factors affecting correlated paternity in plants.     

obitools: a unix‐inspired software package for DNA metabarcoding

DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next‐generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor‐made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools . A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org .     

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

Background  

Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.     

STADEERS: a software package for the statistical design of experiments pertaining to the estimation of parameters in rate expressions that describe enzyme-catalyzed processes

This paper describes a computational algorithm (STADEERS-STAtisticalDesign of Exeriments in Enzyme ReactorS) for the statisticaldesign of biochemical engineering experiments. The type of experimentthat qualifies for this package involves a batch reaction catalyzedby a soluble enzyme where the activity of the enzyme decayswith time. Assuming that both the catalytic action and the deactivationof the enzyme obey known rate expressions, the present codeis helpful in the process of obtaining estimates of the kineticparameters by providing as output the times at which samplesshould be withdrawn from the reacting mixture. Starting D-optimaldesign is used as a basis for the statistical approach. ThisBASIC code is a powerful tool when fitting a rate expressionto data because it increases the effectiveness of experimentationby helping the biochemical kineticist obtain data points withthe largest possible informa tional content.     

MorphoJ: an integrated software package for geometric morphometrics

Increasingly, data on shape are analysed in combination with molecular genetic or ecological information, so that tools for geometric morphometric analysis are required. Morphometric studies most often use the arrangements of morphological landmarks as the data source and extract shape information from them by Procrustes superimposition. The MorphoJ software combines this approach with a wide range of methods for shape analysis in different biological contexts. The program offers an integrated and user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. MorphoJ is written in Java and versions for the Windows, Macintosh and Unix/Linux platforms are freely available from http://www.flywings.org.uk/MorphoJ_page.htm.     

TiLIA: a software package for image analysis of firefly flash patterns

As flash signaling patterns of fireflies are species specific, signal‐pattern analysis is important for understanding this system of communication. Here, we present time‐lapse image analysis (TiLIA), a free open‐source software package for signal and flight pattern analyses of fireflies that uses video‐recorded image data. TiLIA enables flight path tracing of individual fireflies and provides frame‐by‐frame coordinates and light intensity data. As an example of TiLIA capabilities, we demonstrate flash pattern analysis of the fireflies Luciola cruciata and L. lateralis during courtship behavior.